Time-frequency entangled photons ("biphotons") exhibit joint spectral and temporal correlations that are unattainable with classical light. Besides being deployed for tests of quantum nonlocality, these photonic states are desirable for a unique range of applications that can significantly impact communications and computation. In this dissertation, we describe novel schemes based on spectral and temporal domain processing for manipulating and characterizing broadband biphotons. Implementing frequency-dependent filters, first, we present and demonstrate a technique for controlling the relative delay between a pair of entangled photons, relying on pump frequency tuning and the quantum concept of nonlocal dispersion cancellation. Next, we demonstrate near-field frequency-to-time mapping, a technique adopted from classical photonics, for arbitrary control of biphoton temporal correlations. Subsequently, we generate temporal correlation trains by creating biphoton frequency combs through programmable spectral amplitude shaping and demonstrate the temporal Talbot effect with entangled photons for the first time. Moreover, in the absence of fast single-photon detectors, we show how electro-optic phase modulation (originally a time-dependent operation) can be used to examine the coherence of biphoton frequency combs. Lastly, we introduce a scheme based on electro-optic intensity modulation, another time-domain operation, for improving the resolution in biphoton temporal correlation measurements. Overall, our body of work could provide additional insight into the manipulation and characterization of biphoton states, as well as contribute towards the improvement of quantum technologies.